What I've done so far is go into Mocha and made a matte out the the two halves of the blouse and use the tricolor effect in AE and then dropped the opacity slightly to make it look less like a cartoon and added the slightest bit of noise to give it a little more texture.
Problem 1 (The biggest one) - I feathered the edge slightly so it doesn't look like it was cut sharply with scissors, but while it helped with the edge it created wide a black line along the edge that I cannot seem to eliminate which makes it more obvious it is a replacement. It makes it look sort of like I drew a black outline of the area I matted and forgot to erase it. Sort of like when you see a watercolor painting that is done over a pencil or pen drawing.
Problem 2 - I have color issues with the shirt since it was white and now is a bronze color, on the side that is getting hot light through the window I need to graduate it so the light looks more natural. I was thinking I could take care of this by making another under that masks the areas I want darker and make the composition layer slightly translucent so it can be seen.
Problem 3 - Midway through the sequence, the actor turns her head swinging her through the mask and back. Is there a way to key out a white gradient so that I can place her hair swing on a the top layer, just the hair? I haven't had much success with this again because of the white gradient cloth layer rom the original clip.
The answer is probably hard manual masking work for each and every of your problems because based on your description we only can conclude that it was shot wrongly in teh first place. You might try eliminating black fringes with the Remove Color Matting effect, but for your other two problems you will really have to spend some time drawing and animating masks frame by frame. And rrather than looking for easy solutions with tracking that's probably what would have worked better in the first place. Anyway, without seeing a reference shot it's impossible to advise specifically.
If you have accurate animated masks using Mocha, try precomping them to use the results as a track matte for a solid, which you set to the Color blend mode. To change the color of the shirt, change the color of the solid.
If it doesn't work, you're not out much time, which you can then use to ponder Mylenium's always-sound advice.
I am also still rather new to After Effects on a whole, so i hope this is not the wrong information, but check out this four part tutorial from Andrew Devis:
(dont forget the other three parts) - In this series, he explains some great tricks to remove lines and clear spaces around masks. He also provides some great Keying sites that may be used for practice.
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